Touchscreens have gained wide usage in a variety of applications such as smart phones, tablets, portable navigation devices, laptop and desktop computers, portable music players and other general user interfaces and consumer electronic devices, allowing users to intuitively select from prompted options and to perform other user interface operations by simply touching a display screen and a variety of ways. Different touchscreen technologies have been developed, including capacitive, surface capacitance, projected capacitance, resistive, surface acoustic wave touchscreens and others. Touchscreen controllers interface a touchscreen device and a host system, such as a microprocessor of a touchscreen-enabled tablet computer, and can be operated to detect actuations or touches of different locations on the display screen by a user. The touchscreen device is typically configured as an array of rows and columns, and user touches are detected by the controller providing excitation signals to row connections while sensing column connections of the touchscreen device in a panel scanning operation. As with other circuitry in battery-powered portable user devices, touchscreen controller performance and scanning the touchscreen panel can be affected by noise, particularly when connected to battery chargers, where chargers can couple noise into touchscreen devices thereby impacting the ability to detect user touch actuations. The frequency of touch signals are typically close to DC, such as about 10 Hz or less, and theoretically can be separated from the higher frequency charger noise by low-pass filtering. However, the separation is difficult in practice due to aliasing in a multi-rate sampling procedure involving analog-to-digital conversion sampling rates and panel scan rates. In a typical configuration, the touchscreen controller includes one or more analog-to-digital converters operating at a relatively high sampling frequency, with the panel scan operation being performed at a lower frequency. In practice, situations arise in which noise associated with charger operation is aliased into the pass band of a low pass filter, making it difficult to differentiate aliased noise from user touch occurrences. Accordingly, a need remains for improved touchscreen controllers and methods for addressing charger noise and other sources of high-frequency noise.